5DFX | pdb_00005dfx

Structure of the parental state of GAF3 from Slr1393 of Synechocystis sp. PCC6803 (in vivo assembled protein/chromophore)

PDB DOI: https://doi.org/10.2210/pdb5DFX/pdb

Classification: TRANSFERASE
Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-27 Released: 2016-09-14
Deposition Author(s): Xu, X.-L., Zhao, K.-H., Gaertner, W., Hoeppner, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.164 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural elements regulating the photochromicity in a cyanobacteriochrome

Xu, X.-L., Hoeppner, A., Wiebeler, C., Zhao, K.-H., Schapiro, I., Gaertner, W.

(2020) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.1910208117

Macromolecule Content

Total Structure Weight: 25.45 kDa
Atom Count: 1,530
Modeled Residue Count: 158
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine kinase	A	215	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: slr1393 EC: 2.7.13.3
UniProt
Find proteins for P73184 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73184 Go to UniProtKB: P73184
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73184
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.164 (Depositor), 0.180 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.12	α = 90
b = 63.12	β = 90
c = 118.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2020-01-29
Changes: Database references
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.